{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T06:24:08Z","timestamp":1762928648449},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2019,1,14]],"date-time":"2019-01-14T00:00:00Z","timestamp":1547424000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Institut de Biologie Computationnelle ANR","award":["ANR-11-BINF-0002"],"award-info":[{"award-number":["ANR-11-BINF-0002"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The visualization and interpretation of evolutionary spatiotemporal scenarios is broadly and increasingly used in infectious disease research, ecology or agronomy. Using probabilistic frameworks, well-known tools can infer from molecular data ancestral traits for internal nodes in a phylogeny, and numerous phylogenetic rendering tools can display such evolutionary trees. However, visualizing such ancestral information and its uncertainty on the tree remains tedious. For instance, ancestral nodes can be associated to several geographical annotations with close probabilities and thus, several migration or transmission scenarios exist.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We expose a web-based tool, named AQUAPONY, that facilitates such operations. Given an evolutionary tree with ancestral (e.g. geographical) annotations, the user can easily control the display of ancestral information on the entire tree or a subtree, and can view alternative phylogeographic scenarios along a branch according to a chosen uncertainty threshold. AQUAPONY interactively visualizes the tree and eases the objective interpretation of evolutionary scenarios. AQUAPONY\u2019s implementation makes it highly responsive to user interaction, and instantaneously updates the tree visualizations even for large trees (which can be exported as image files).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>AQUAPONY is coded in JavaScript\/HTML, available under Cecill license, and can be freely used at http:\/\/www.atgc-montpellier.fr\/aquapony\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz011","type":"journal-article","created":{"date-parts":[[2019,1,11]],"date-time":"2019-01-11T04:23:14Z","timestamp":1547180594000},"page":"3163-3165","source":"Crossref","is-referenced-by-count":3,"title":["AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees"],"prefix":"10.1093","volume":"35","author":[{"given":"Bastien","family":"Cazaux","sequence":"first","affiliation":[{"name":"Universit\u00e9 Montpellier Department of Computer Science, LIRMM, UMR 5506, CNRS and , Montpellier, France"},{"name":"Institut de Biologie Computationelle , Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guillaume","family":"Castel","sequence":"additional","affiliation":[{"name":"Institut de Biologie Computationelle , Montpellier, France"},{"name":"Forest, Grassland and Freshwater Ecology , CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, , Montpellier, France"},{"name":"Univ Montpellier , CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, , Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Rivals","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Montpellier Department of Computer Science, LIRMM, UMR 5506, CNRS and , Montpellier, France"},{"name":"Institut de Biologie Computationelle , Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,1,14]]},"reference":[{"key":"2023062711312765700_btz011-B1","doi-asserted-by":"crossref","first-page":"2910","DOI":"10.1093\/bioinformatics\/btr481","article-title":"Spread: spatial phylogenetic reconstruction of evolutionary dynamics","volume":"27","author":"Bielejec","year":"2011","journal-title":"Bioinformatics"},{"key":"2023062711312765700_btz011-B2","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1186\/1471-2105-7-439","article-title":"Treedyn: towards dynamic graphics and annotations for analyses of trees","volume":"7","author":"Chevenet","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023062711312765700_btz011-B3","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1093\/bioinformatics\/btq086","article-title":"Scriptree: scripting phylogenetic graphics","volume":"26","author":"Chevenet","year":"2010","journal-title":"Bioinformatics"},{"key":"2023062711312765700_btz011-B4","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1093\/molbev\/msi103","article-title":"Bayesian coalescent inference of past population dynamics from molecular sequences","volume":"22","author":"Drummond","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"2023062711312765700_btz011-B5","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1093\/bioinformatics\/btk051","article-title":"Lamarc 2.0: maximum likelihood and Bayesian estimation of population parameters","volume":"22","author":"Kuhner","year":"2006","journal-title":"Bioinformatics"},{"key":"2023062711312765700_btz011-B6","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1093\/bioinformatics\/btg180","article-title":"MrBayes 3: Bayesian phylogenetic inference under mixed models","volume":"19","author":"Ronquist","year":"2003","journal-title":"Bioinformatics"},{"key":"2023062711312765700_btz011-B7","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.meegid.2014.01.001","article-title":"Global phylogeography of dengue type 1 and 2 viruses reveals the role of India","volume":"22","author":"Walimbe","year":"2014","journal-title":"Infect. Genet. Evol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/17\/3163\/50719895\/bioinformatics_35_17_3163.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/17\/3163\/50719895\/bioinformatics_35_17_3163.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T11:32:17Z","timestamp":1687865537000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/17\/3163\/5289326"}},"subtitle":[],"editor":[{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,1,14]]},"references-count":7,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2019,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz011","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,9,1]]},"published":{"date-parts":[[2019,1,14]]}}}